BACKGROUND: Although heart rate variability (HRV) is widely used to assess cardiac autonomic function, few studies have specifically investigated nocturnal HRV. OBJECTIVE: The purpose of this study was to assess the association between nocturnal HRV and cardiovascular disease (CVD) incidence over 4 years in a population-based sample. METHODS: A total of 1784 participants (48.2% men; 58 +/- 11 years) from the HypnoLaus population-based cohort free of CVD at baseline were included. Polysomnography-based electrocardiograms were exported to analyze time- and frequency-domain HRV, Poincare plots indices, detrended fluctuation analysis, acceleration capacity (AC) and deceleration capacity (DC), entropy, heart rate fragmentation (HRF), and heart rate turbulence. Multivariable-adjusted Cox regression analysis was used to assess the association between HRV indices and incident CVD events. RESULTS: Sixty-seven participants (3.8%) developed CVD over mean follow-up of 4.1 +/- 1.1 years. In a fully adjusted model, AC (hazard ratio per 1-SD increase; 95% confidence interval: 1.59; 1.17-2.16; P = .004), DC (0.63; 0.47-0.84; P = .002), and HRF (1.41; 1.11-1.78; P = .005) were the only HRV metrics significantly associated with incident CVD events after controlling for false discovery rate. CONCLUSION: Nocturnal novel HRV parameters such as AC, DC, and HRF are better predictors of CVD events than time and frequency traditional HRV parameters. These findings suggest a form of dysautonomia and fragmented rhythms, but further experimental studies are needed to delineate the underlying physiological mechanisms of these novel HRV parameters.